GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Streptacidiphilus oryzae TH49

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_051939905.1 BS73_RS13630 branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>NCBI__GCF_000744815.1:WP_051939905.1
          Length = 348

 Score =  120 bits (302), Expect = 5e-32
 Identities = 89/303 (29%), Positives = 139/303 (45%), Gaps = 34/303 (11%)

Query: 92  RWAVLALVVVAFVWPFFA------------SRGAVDIATLILIYVMLGIGLNIVVGLAGL 139
           RW    L++V  + P+ A            S G + +  L L++  L  G ++++G  GL
Sbjct: 2   RWWPAPLLLVLLIAPYSAVPLPGLLDGPIGSAGNLQLIALCLVFGGLATGYDLLLGRTGL 61

Query: 140 LDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIV 199
           L  G+  ++A G Y   +L   AG  F  A  +      L   +LG   LR+ G   ++V
Sbjct: 62  LSFGHALYFATGTYVTDVLMLRAGLPFAAAAVLGLAAGVLLAAVLGSVSLRVTGIGFSMV 121

Query: 200 TLGFGEIIRILL-RNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNT 258
           TL F +   IL+ R+    TGG  G+ +             R P  +       GI +  
Sbjct: 122 TLAFAQAGSILVTRDPGGATGGEEGLAAPAD----------RMPAAL------IGIGHTA 165

Query: 259 NYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFT 318
           +     LY +AL  V+L   V+  L+R PIGR WE ++E+E+    LGL P   KL+AF 
Sbjct: 166 D-----LYWIALAYVVLTFAVVQWLLRSPIGRVWEGIKENELRVEVLGLRPHGFKLAAFV 220

Query: 319 IGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE 378
           +  + A   G  +    G  TP++ T   +  +L +VVLGG GS+ G +L  V+     +
Sbjct: 221 LSGALAALGGVVYLLLTGGATPQTTTSDFTLSLLVMVVLGGSGSRWGPLLGGVLYTWADQ 280

Query: 379 MRG 381
             G
Sbjct: 281 RLG 283


Lambda     K      H
   0.330    0.146    0.439 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 395
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 348
Length adjustment: 30
Effective length of query: 387
Effective length of database: 318
Effective search space:   123066
Effective search space used:   123066
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory